• ALGAE
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• v.33 no.3
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• pp.205-214
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• 2018

Red algae in the genus Portieria produce secondary halogenated monoterpenes, which are effective deterrents against herbivores, as secondary metabolites. Portieria hornemannii samples from various sites contain different concentrations of these metabolites, suggesting the existence of genetic diversity and cryptic species. To evaluate the genetic diversity and species distribution of Portieria in the northwest Pacific, we analyzed rbcL sequences of samples collected from Korea, Japan, and Taiwan. The phylogenetic analysis revealed five distinct lineages at the species level. One was recognized as Portieria japonica and the others were cryptic lineages in P. hornemannii. The rbcL haplotypes of P. japonica were genetically fragmented into two subgroups of geographic origin; Korean and Japanese. The four cryptic lineages within P. hornemannii were also geographically structured at a much finer scale. These results suggest that different genetic lineages in Portieria evolved from variable microhabitats, consequently influencing secondary metabolites. Further study is required to resolve the relationships between genetic and secondary metabolite variations in Portieria.

• ALGAE
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• v.26 no.1
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• pp.21-32
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• 2011

Studies of the red algal genus Bostrychia over the last 15 years have made it a model system for many evolutionary processes within red algal species. The combination of newly developed, or first employed methods, in red algal species studies has made Bostrychia a pioneer genus in intraspecific studies. Bostrychia was the first genus in which a mitochondrial marker was used for intraspecific red algal phylogeny, and the first for which a 3-genome phylogeny was undertaken. The genus was the first red alga used to genetically show maternal plastid and mitochondria inheritance, and also to show correlation between cryptic species (genetically divergent intraspecific lineages) and reproductive incompatibility. The chemotaxonomic use, and physiological function of osmolytes, has also been extensively studied in Bostrychia. Our continuous studies of Bostrychia also highlight important aspects in algal species studies. Our worldwide sampling, and resampling in certain areas, show that intensive sampling is needed to accurately assess the genetic diversity and therefore phylogeographic history of algal species, with increased sampling altering evolutionary hypotheses. Our studies have also shown that long-term morphological character stability (stasis) and character convergence can only be correctly assessed with wide geographic sampling of morphological species. While reproductive incompatibility of divergent lineages supports the biological species nature of these lineages, reproductive incompatibility is also seen between isolates with little genetic divergence. It seems that reproductive incompatibility may evolve quickly in red algae and the unique early stages of fertilization (e.g., gametes covered by walls, active movement of spermatium nuclei to the distant egg nucleus), also well investigated in Bostrychia,. may be key to our understanding of this process.

• Journal of Life Science
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• v.13 no.2
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• pp.175-183
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• 2003

The chimpanzee and gorilla are classified into hominidae, catarrhini, primates. These species are originated from Africa, so called African great apes. Recently, primatologists have classified that there are 2 species 5 subspecies of the chimpanzee and gorilla, respectively. Since the human genome project has been finished, the chimpanzee genome project has been launched to understand human evolution and genetic diseases. The sequences of chimpanzee chromosome 22 homologous to human chromosome 21 were completed, and then the Y chromosome of chimpanzee is being analyzed. Comparative analysis of human, chimpanzee and gorilla could provide the key for understanding of various human diseases and human origin. By detecting human specific-functional genes or mobile genetic elements (HERV, LINE, SINE) through primate research, we could understand what is human being\ulcorner gradually, For these comparative researches, we summarized fundamental knowledge of the feature, phylogeny and evolution of African great apes including humans.

• Parasites, Hosts and Diseases
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• v.55 no.1
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• pp.31-37
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• 2017

This study aimed to investigate the morphology and reconstruct the phylogenetic relationships of Centrocestus formosanus originating from 5 species of freshwater fish, i.e., Esomus metallicus, Puntius brevis, Anabas testudineus, Parambassis siamensis, and Carassius auratus, in Chiang Mai province, Thailand. Sequence-related amplified polymorphism (SRAP) and phylogeny based on internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (CO1) were performed. The results showed similar morphologies of adult C. formosanus from day 5 after infection in chicks. C. formosanus originated from 4 species of freshwater fish had the same number of circumoral spines on the oral sucker, except for those from C. auratus which revealed 34 circumoral spines. The phylogenetic tree obtained from SRAP profile and the combination of ITS2 and CO1 sequence showed similar results that were correlated with the number of circumoral spines in adult worms. Genetic variability of C. formosanus also occurred in different species of freshwater fish hosts. However, more details of adult worm morphologies and more sensitive genetic markers are needed to confirm the species validity of C. formosanus with 34 circumoral spines originating from C. auratus in the future.

• ALGAE
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• v.31 no.3
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• pp.219-230
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• 2016

The Euglena deses group are common freshwater species composed of E. adhaerens, E. carterae, E. deses, E. mutabilis, and E. satelles. These species are characterized by elongated cylindrical worm-like cell bodies and numerous discoid chloroplasts with a naked pyrenoid. To understand the cryptic diversity, species delimitation and phylogenetic relationships among members of the group, we analyzed morphological data (light and scanning electron microscopy) and molecular data (nuclear small subunit [SSU] and large subunit [LSU] rDNAs and plastid SSU and LSU rDNAs). Bayesian and maximum likelihood analyses based on the combined four-gene dataset resulted in a tree consisting of two major clades within the group. The first clade was composed of two subclades: the E. mutabilis subclade, and the E. satelles, E. carterae, and E. adhaerens subclade. The E. mutabilis subclade was characterized by a lateral canal opening at the anterior end and a single pellicular stria, whereas the E. satelles, E. carterae, and E. adhaerens subclade was characterized by an apical canal opening at the anterior end of the cell and double pellicular striae. The second clade consisted of 20 strains of E. deses, characterizing by a subapical canal opening at the anterior end and double pellicular striae, but they showed cell size variation and high genetic diversity. Species boundaries were tested using a Bayesian multi-locus species delimitation method, resulting in the recognition of five cryptic species within E. deses clade.

• Fisheries and Aquatic Sciences
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• v.24 no.5
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• pp.181-190
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• 2021

Grouper is one of the most economically important fishes with various morphological forms and characteristics, meaning it is often difficult to identify species and distinguish between life stages, sometimes leading to morphological misidentification. Therefore, identification using a molecular deoxyribose nucleic acid (DNA) approach was needed as an alternative means to identify closely related species. This study aims to determine the molecular phylogeny of grouper from the northern part of the Bird's Head Seascape of Papua. The DNA sequence of each cytochrome oxidase I (COI) gene was used to study the molecular relationship among closely related species of grouper. The results showed that there were 16 Epinephelinae that have been compared to a gene bank (National Centre for Biotechnology Information, NCBI) in the sequence length of 623 base pairs. The closest genetic distance was found between Cephalopholis miniata and Cephalopholis sexmaculata (0.036), while the furthest genetic distance was observed between Plectropomus laevis and Cephalopholis spiloparaea (0.247). This finding was further reinforced by the morphological characters of each species. This finding highlighted that five genera were represented as a monophyletic group (clade), i.e., Epinephelus, Cephalopholis, Plectropomus, Saloptia and Variola.

• Journal of Veterinary Science
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• v.22 no.5
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• pp.73.1-73.11
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• 2021

Background: Feline calicivirus (FCV) is a common pathogen of felids, and FCV vaccination is regularly practiced. The genetic variability and antigenic diversity of FCV hinder the effective control and prevention of infection by vaccination. Improved knowledge of the epidemiological characteristics of FCV should assist in the development of more effective vaccines. Objectives: This study aims to determine the prevalence of FCV in a population of cats with FCV-suspected clinical signs in Hangzhou and to demonstrate the antigenic and genetic relationships between vaccine status and representative isolated FCV strains. Methods: Cats (n = 516) from Hangzhou were investigated between 2018 and 2020. The association between risk factors and FCV infection was assessed. Phylogenetic analyses based on a capsid coding sequence were performed to identify the genetic relationships between strains. In vitro virus neutralization tests were used to assess antibody levels against isolated FCV strains in client-owned cats. Results: The FCV-positive rate of the examined cats was 43.0%. Risk factors significantly associated with FCV infection were vaccination status and oral symptoms. Phylogenetic analysis revealed a radial phylogeny with no evidence of temporal or countrywide clusters. There was a significant difference in the distribution of serum antibody titers between vaccinated and unvaccinated cats. Conclusions: This study revealed a high prevalence and genetic diversity of FCV in Hangzhou. The results indicate that the efficacy of FCV vaccination is unsatisfactory. More comprehensive and refined vaccination protocols are an urgent and unmet need.

• Molecules and Cells
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• v.20 no.1
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• pp.151-156
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• 2005

The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.

• Korean Journal of Ecology and Environment
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• v.36 no.3 s.104
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• pp.221-234
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• 2003

Phylogenetic studies would clarify the diversity of fishes if the morphological analysis based on plesimorphy characters combined with new genetic analysis on molecular level, inferring more accurate and objective phylogeny and the taxonomy. Current molecular phylogenetic approach using mitochondrial genome provides the framework for a new hypothesis not only inferring the relationships between ancestor descendants but raveling the intra-, interspecies variation.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.2
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• pp.173-180
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• 2011

Osteocalcin (OC), a marker of bone turnover, displays patterns in relation to physiological and genetic factors. Here, we present an association study in a population of Chinese Holstein cattle (n = 24) with OC serum concentration as a phenotypic trait. We hypothesised that OC status is associated with phylogeny, vitamin D serum level and single nucleotide polymorphisms (SNPs). Mitochondrial DNA (mtDNA) was used as an unlinked marker to examine phylogeny and linkage to measured phenotypic traits of vitamin D and OC status. Following an association study with OC serum variability as the trait, genotyping of SNPs (n = 27) in OC-related genes was performed. Candidate SNPs were chosen in genes with an emphasis on the vitamin D and vitamin K pathways. Multivariant factor analysis revealed a correlation between vitamin D serum concentration and a SNP in the gene GC (rs43338565), which encodes a vitamin D-binding protein, as well as between a SNP in NFATc1 (rs42038422) and OC concentration. However, univariate analysis revealed that population structure, vitamin D serum levels and SNPs were not significant determinants of OC status in the studied group.